Mercurial > repos > iuc > mothur_tree_shared

comparison tree.shared.xml @ 3:8d6cd6767107 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
author iuc
date Wed, 14 Feb 2018 09:37:37 -0500
parents a16c10c1c418
children 466897b7c726
comparison
equal deleted inserted replaced
2:d73991c11767 3:8d6cd6767107
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <expand macro="version_command"/> 8 <expand macro="version_command"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@ 10 @SHELL_OPTIONS@
11 11
12 ## create symlinks to input datasets 12 ## create symlinks to input datasets
13 ln -s "$input.dist" input_dist.dat && 13 ln -s '$input.dist' input_dist.dat &&
14 #if not $input.source == "shared": 14 #if not $input.source == "shared":
15 ln -s "$input.name" input_name.dat && 15 ln -s '$input.name' input_name.dat &&
16 #end if
17
18 echo 'tree.shared(
19 #if $input.source == "shared":
20 shared=input_dist.dat,
21 #if $input.groups:
22 groups=${ str($input.groups).replace(",","-") },
16 #end if 23 #end if
17 24 #if $input.label:
18 echo 'tree.shared( 25 label=${ str($input.label).replace(",","-") },
19 #if $input.source == "shared": 26 #end if
20 shared=input_dist.dat, 27 #if $input.subsampling.use == "yes":
21 #if $input.groups: 28 #if $input.subsampling.subsample:
22 groups=${ str($input.groups).replace(",","-") }, 29 subsample=$input.subsampling.subsample,
23 #end if
24 #if $input.label:
25 label=${ str($input.label).replace(",","-") },
26 #end if
27 #if $input.subsampling.use == "yes":
28 #if $input.subsampling.subsample:
29 subsample=$input.subsampling.subsample,
30 #else
31 subsample=T,
32 #end if
33 #if $input.subsampling.iters:
34 iters="$input.subsampling.iters,
35 #end if
36 #end if
37 #elif $input.source == "column":
38 column=input_dist.dat,
39 name=input_name.dat,
40 #elif $input.source == "phylip":
41 phylip=input_dist.dat,
42 #if $input.name:
43 name=input_name.dat,
44 #end if
45 #else 30 #else
46 count=input_name.dat, 31 subsample=T,
47 #end if 32 #end if
48 #if $calc: 33 #if $input.subsampling.iters:
49 calc=${ str($calc).replace(",","-") }, 34 iters="$input.subsampling.iters,
50 #end if 35 #end if
51 processors='\${GALAXY_SLOTS:-8}' 36 #end if
52 )' 37 #elif $input.source == "column":
53 | sed 's/ //g' ## mothur trips over whitespace 38 column=input_dist.dat,
54 | mothur 39 name=input_name.dat,
55 | tee mothur.out.log 40 #elif $input.source == "phylip":
41 phylip=input_dist.dat,
42 #if $input.name:
43 name=input_name.dat,
44 #end if
45 #else
46 count=input_name.dat,
47 #end if
48 #if $calc:
49 calc=${ str($calc).replace(",","-") },
50 #end if
51 processors='\${GALAXY_SLOTS:-8}'
52 )'
53 | sed 's/ //g' ## mothur trips over whitespace
54 | mothur
55 | tee mothur.out.log
56 ]]></command> 56 ]]></command>
57 <inputs> 57 <inputs>
58 <conditional name="input"> 58 <conditional name="input">
59 <param name="source" type="select" label="Select input format"> 59 <param name="source" type="select" label="Select input format">
60 <option value="shared">OTU Shared</option> 60 <option value="shared">OTU Shared</option>
150 <param name="name" value="amazon1.names"/> 150 <param name="name" value="amazon1.names"/>
151 <output name="tre" md5="33cc8cb433f123e49b33b998186b74ed" ftype="mothur.tre"/> 151 <output name="tre" md5="33cc8cb433f123e49b33b998186b74ed" ftype="mothur.tre"/>
152 <expand macro="logfile-test"/> 152 <expand macro="logfile-test"/>
153 </test> 153 </test>
154 </tests> 154 </tests>
155 <help> 155 <help><![CDATA[
156 <![CDATA[
157 156
158 @MOTHUR_OVERVIEW@ 157 @MOTHUR_OVERVIEW@
159 158
160 **Command Documentation** 159 **Command Documentation**
161 160
162 The tree.shared_ command will generate a newick-formatted tree file that describes the dissimilarity (1-similarity) among multiple groups. For calc parameter choices see: https://www.mothur.org/wiki/Calculators 161 The tree.shared_ command will generate a newick-formatted tree file that describes the dissimilarity (1-similarity) among multiple groups. For calc parameter choices see: https://www.mothur.org/wiki/Calculators
163 162
164 .. _tree.shared: https://www.mothur.org/wiki/Tree.shared 163 .. _tree.shared: https://www.mothur.org/wiki/Tree.shared
165 164
166 ]]> 165 ]]></help>
167 </help>
168 <expand macro="citations"/> 166 <expand macro="citations"/>
169 </tool> 167 </tool>